White Matter Mask Generation

3

Hi, Donald,

The problem is that: [ERROR] input images do not have the same number of dimensions.

t1_mpr_ns_sag_iso_5TT_nocrop_WM_axis3_wrped.nii.gz (176x224x256)
DTI_30_average-6.nii (128 x 128 x 44 x 186)

I wonder if there is a method to resample the 3rd volume of 5TT image to 128x128x44, so that I can use it as a white matter mask?

The information of both scans is shown below in the images:

image

image

Here are my current commands:

  1. 5ttgen fsl t1_mpr_ns_sag_iso.nii.gz t1_mpr_ns_sag_iso_5TT_nocrop.mif -nocrop

  2. extract the 3rd volume (WM volume):
    mrconvert -coord 3 2 t1_mpr_ns_sag_iso_5TT_nocrop.mif t1_mpr_ns_sag_iso_5TT_nocrop_WM.nii.gz

  3. reduce 4D image to 3D image:
    mrmath t1_mpr_ns_sag_iso_5TT_nocrop_WM.nii.gz mean -axis 3
    t1_mpr_ns_sag_iso_5TT_nocrop_WM_axis3.nii.gz

  4. Register t1_mpr_ns_sag_iso_5TT_nocrop_WM_axis3.nii.gz to DTI_30_average-6.mif

Thanks,
Chaoqing